Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010021.1 Corchorus capsularis cultivar CVL-1 contig10042, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21042
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3763 original size:5 final size:5
Alignment explanation
Indices: 3737--3774 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
3727 CACTTCAAAG
3737 AAAT- AAATA TAAATA TAAATA AAATA AAATA AAATA AA
1 AAATA AAATA -AAATA -AAATA AAATA AAATA AAATA AA
3775 GAGATAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.12
5 17 0.53
6 11 0.34
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAATA
Found at i:6194 original size:19 final size:19
Alignment explanation
Indices: 6139--6196 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
6129 CATGATGATC
6139 CTTGAGTCATGTAGATCAT
1 CTTGAGTCATGTAGATCAT
* *
6158 CTTG-GTAAAG-ATGATCAT
1 CTTGAGTCATGTA-GATCAT
6176 CTTGAGTCATGTAGATCAT
1 CTTGAGTCATGTAGATCAT
6195 CT
1 CT
6197 CAATTGGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.03
18 14 0.44
19 16 0.50
20 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (19 bp):
CTTGAGTCATGTAGATCAT
Found at i:8869 original size:15 final size:16
Alignment explanation
Indices: 8849--8878 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8839 TTATTTTTAG
8849 ATTATAATA-TATTAA
1 ATTATAATATTATTAA
8864 ATTATAATATTATTA
1 ATTATAATATTATTA
8879 TTTATAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAATATTATTAA
Found at i:9878 original size:341 final size:336
Alignment explanation
Indices: 9455--10070 Score: 817
Period size: 341 Copynumber: 1.8 Consensus size: 336
9445 TCGGGGTTCA
* * * *
9455 GGCTCAATTTTGCATGATTTTTGGCTCCGAGACTACTTGAAATATCTATATTCTTCTAAACAAAT
1 GGCTCAATTTTGCATGATTTTTGGCGCCAAGACTACTTGAAATATCAATATTCATCTAAACAAAT
* * *
9520 CTCAGCCACATTGGATTTAA-AGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTA
66 CTCAGCCACATTGGATTTAAGA-ATTTATTTTTAAAAGCATCTGAATCTTCTTTCGATTTAATTA
** * * * * *
9584 GAAATTAATTTGGAAAAAAAAAGGAAAATGATATTAGAAACGTCAAAAGCCCTTCAA-TTTTTGG
130 GAAATTAATTCAG-AAAAAAAAGAAAAACGATATTACAAACGTCAAAAACCCTCCAACTTTTTGG
* ** *
9648 CATTGAATTATATATATTTTTTTATGAGTATTTTTTAGTCAAAAATTGAG-GAAATATCTTTCGA
194 CATTAAATTATATATA---TTTTATGAGTA--TTTTAACCAAAAATTGAGAAAAATAT-TTTCGA
9712 GTCAATTTTTACAAAATTTTAGCCAAAATTGTGTAATAAACATCACAATTTTTAGATAAAAAATT
253 GTCAATTTTTACAAAATTTTAGCCAAAATTGTGTAATAAACATCACAATTTTTAGATAAAAAATT
9777 GTTATGATCTACGGGCCCC
318 GTTATGATCTACGGGCCCC
* * * *
9796 GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-AAGATATCAATATTCATGTAATCAAA
1 GGCTCAATTTTGCATGATTTTTGGCGCCAAGACTACTTGAA-ATATCAATATTCATCTAAACAAA
*
9860 TCTCAGCCACATTGGATTTAAGAATTTATTTTTAAAAGCATCTGAATCTTCTTTCGATTTAATTG
65 TCTCAGCCACATTGGATTTAAGAATTTATTTTTAAAAGCATCTGAATCTTCTTTCGATTTAATTA
* * * * *
9925 GAAATTAATTCAGTAAAATATGAAAAACGATATTACAAACGTGAAAAATCCTCCAATCTTTTTGG
130 GAAATTAATTCAGAAAAAAAAGAAAAACGATATTACAAACGTCAAAAACCCTCCAA-CTTTTTGG
* * **
9990 CGTTAAATTATATATATTTTATGAGTATTTTAACCAAAAATTGAGAAAAATATTTTCGGGTCTTT
194 CATTAAATTATATATATTTTATGAGTATTTTAACCAAAAATTGAGAAAAATATTTTCGAGTCAAT
*
10055 TTTTGCAAAATTTTAG
259 TTTTACAAAATTTTAG
10071 TCGAAATCAT
Statistics
Matches: 237, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
337 40 0.17
338 6 0.03
339 11 0.05
340 35 0.15
341 123 0.52
342 22 0.09
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (336 bp):
GGCTCAATTTTGCATGATTTTTGGCGCCAAGACTACTTGAAATATCAATATTCATCTAAACAAAT
CTCAGCCACATTGGATTTAAGAATTTATTTTTAAAAGCATCTGAATCTTCTTTCGATTTAATTAG
AAATTAATTCAGAAAAAAAAGAAAAACGATATTACAAACGTCAAAAACCCTCCAACTTTTTGGCA
TTAAATTATATATATTTTATGAGTATTTTAACCAAAAATTGAGAAAAATATTTTCGAGTCAATTT
TTACAAAATTTTAGCCAAAATTGTGTAATAAACATCACAATTTTTAGATAAAAAATTGTTATGAT
CTACGGGCCCC
Found at i:10798 original size:332 final size:333
Alignment explanation
Indices: 10123--10991 Score: 834
Period size: 332 Copynumber: 2.6 Consensus size: 333
10113 CTAGACACCT
* * ** * * * * * * *
10123 TGAAATATCTATGTTCATCTAATTAAATCTCAGCCATATTGCAGTTAAGAATTTGTTTTTACGAG
1 TGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG-AGTTATTGTAACGAG
* * * * * *
10188 CA-TCTAAATCTTGTTTCAATTTAATTAGAAATAAATTTAGAAAAATATGAAAAACGATATTGAA
65 CATTCTGAATCATGTTTCGATTTAATTAGAAATTAATTTAGGAAAATATGAAAAACGATATTAAA
** ** * * *
10252 AGCGTGAAAAGTCCTCCAATCTTTTTGGAATTGAATTATATATA-TTT-T--CTA----GGC-AA
130 AGAATGAAAAACCCTCCAATCTTTTTGGCATTGACTTATATATATTTTATGAGTATTGTGGCAAA
** *
10308 AAATTGAGGAAAAATATTTCTGATCAATTTTTGCAAAATATTAGCTGAAATCGTGTACATTAGTC
195 AAATTGAGGAAAAATATTTCTGATCAATTTTTGCAAAATATTAGCCAAAATCGTGTACATTAATC
* * * *
10373 AAAATCATGGTTTTTGGCTAAAAGTACGTGCCGGGGCCCCGGTTCAGTGTTGCATGATTTTTGGC
260 --AATCACGGTTTTTGGCTAAAAG-ACATGCCGGGGCCCCGGCTAAGTGTTGCATGATTTTTGGC
* * *
10438 GCCGAGACTCCG
322 ACCAAGAATCCG
* *
10450 TGAAATATATATATTCATCTAACCAAATTTCAGCCACATTGGATTTAAG-GTT-TTGTAAGGTAA
1 TGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAGTTATTGTAACG--A
*
10513 GCA-TCTGAATCATGTTTCGATTTAATTAGAAATTAA-TTCGGAAAATAATAGGAAAAACGATAT
64 GCATTCTGAATCATGTTTCGATTTAATTAGAAATTAATTTAGGAAAAT-AT--GAAAAACGATAT
* *
10576 TAGAAGAAT-AAAAAGCCCTTCAATCTTTTTGGCATTGAACTT-TATA-ATTTTTATGAGTATTG
126 TAAAAGAATGAAAAA-CCCTCCAATCTTTTTGGCATTG-ACTTATATATA-TTTTATGAGTATTG
*
10638 TGGCTAAAAATTGAGGAAATAA-ATTTC-GAGTCAATTTTTGCAAAAT-TCTAGCCAAAATCGTG
188 TGGCAAAAAATTGAGGAAA-AATATTTCTGA-TCAATTTTTGCAAAATAT-TAGCCAAAATCGTG
* * *
10700 TA-A-TAATC-ATCACGGTTTTTTGGCTAAAACG-CATTCCGGGGCCTCGGCTAAGTTTTGCATG
250 TACATTAATCAATCACGG-TTTTTGGCTAAAA-GACATGCCGGGGCCCCGGCTAAGTGTTGCATG
* **
10761 ATTTTTGGCATCAAGAATCTT
313 ATTTTTGGCACCAAGAATCCG
* * * * * *
10782 TGAAATAT-TCATATTCATCTAATCAAATCTCAGCTACTTTGGATTTAAGAATTTATTTTTACGA
1 TGAAATATAT-ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG-AGTTATTGTAACGA
* * *
10846 GCATTTTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGGAAAATATGAAAAATGATATTAA
64 GCATTCTGAATCATGTTTCGATTTAATTAGAAATTAATTTAGGAAAATATGAAAAACGATATTAA
** * * * *
10911 AAGCGTGAAAAATCCTCCAATCTTTTTGGCGTTGACTTATATATATTTTATGAGTATTTTTGCAA
129 AAGAATGAAAAACCCTCCAATCTTTTTGGCATTGACTTATATATATTTTATGAGTATTGTGGCAA
*
10976 AAAAATGAGGAAAAAT
194 AAAATTGAGGAAAAAT
10992 CTTTTGGGTC
Statistics
Matches: 444, Mismatches: 66, Indels: 59
0.78 0.12 0.10
Matches are distributed among these distances:
324 5 0.01
325 10 0.02
326 35 0.08
327 46 0.10
328 40 0.09
329 6 0.01
330 1 0.00
331 7 0.02
332 159 0.36
333 23 0.05
334 36 0.08
335 18 0.04
336 7 0.02
337 49 0.11
338 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (333 bp):
TGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAGTTATTGTAACGAGC
ATTCTGAATCATGTTTCGATTTAATTAGAAATTAATTTAGGAAAATATGAAAAACGATATTAAAA
GAATGAAAAACCCTCCAATCTTTTTGGCATTGACTTATATATATTTTATGAGTATTGTGGCAAAA
AATTGAGGAAAAATATTTCTGATCAATTTTTGCAAAATATTAGCCAAAATCGTGTACATTAATCA
ATCACGGTTTTTGGCTAAAAGACATGCCGGGGCCCCGGCTAAGTGTTGCATGATTTTTGGCACCA
AGAATCCG
Found at i:19915 original size:2 final size:2
Alignment explanation
Indices: 19908--19937 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19898 CAGGGTCATC
19908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19938 AAATAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.